On 11/19/19 10:30 PM, Iman Katouzian wrote:
Good day. I have encountered a problem in my protein-ligand simulation as after the energy minimization step, when I run the gmx mdrun -deffnm nvt I encounter the error segmentation faiulire core dumped : step 1: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step1b.pdb to ./#step1b.pdb.8# Back Off! I just backed up step1c.pdb to ./#step1c.pdb.8# Wrote pdb files with previous and current coordinates *Segmentation fault (core dumped)*
http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 [email protected] | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
